Variant report

Variant	rs56052250
Chromosome Location	chr3:53874372-53874373
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1025690	0.88[EUR][1000 genomes]
rs10510765	1.00[ASN][1000 genomes]
rs10510766	1.00[ASN][1000 genomes]
rs11705918	1.00[ASN][1000 genomes]
rs11706303	1.00[ASN][1000 genomes]
rs11708227	1.00[ASN][1000 genomes]
rs11709505	1.00[ASN][1000 genomes]
rs11719179	1.00[ASN][1000 genomes]
rs13075639	1.00[ASN][1000 genomes]
rs13076366	1.00[ASN][1000 genomes]
rs13082692	1.00[ASN][1000 genomes]
rs13092344	1.00[ASN][1000 genomes]
rs17053532	1.00[ASN][1000 genomes]
rs17641133	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2118421	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2125876	1.00[ASN][1000 genomes]
rs2232333	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276839	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2289205	0.89[EUR][1000 genomes]
rs2359204	1.00[ASN][1000 genomes]
rs2633726	1.00[ASN][1000 genomes]
rs28675949	1.00[ASN][1000 genomes]
rs35377175	1.00[ASN][1000 genomes]
rs35414202	1.00[ASN][1000 genomes]
rs35657034	1.00[ASN][1000 genomes]
rs3755817	0.89[EUR][1000 genomes]
rs4453827	1.00[ASN][1000 genomes]
rs4546140	0.85[EUR][1000 genomes]
rs45560831	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45616236	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55974100	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73092085	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1003204	chr3:53820070-53877149	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv876803	chr3:53822893-53889849	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv518466	chr3:53832903-53882663	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv521181	chr3:53833509-53881471	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
9	nsv1010575	chr3:53846741-53934781	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
11	nsv997771	chr3:53852695-53926635	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
12	nsv1002141	chr3:53858541-53934781	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
13	nsv876805	chr3:53865731-53883722	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56052250	CHDH	cis	Nerve Tibial	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53839600-53876600	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr3:53846600-53879800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:53849600-53875400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:53852400-53878200	Weak transcription	Hela-S3	cervix
5	chr3:53853400-53877200	Weak transcription	Colonic Mucosa	Colon
6	chr3:53853800-53879000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:53854000-53879400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:53854200-53877400	Weak transcription	Esophagus	oesophagus
9	chr3:53854400-53876400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:53856800-53879200	Weak transcription	Ovary	ovary
11	chr3:53857400-53876400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr3:53857400-53876800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:53858200-53876400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:53858600-53876400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:53859000-53876400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:53861000-53876400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr3:53861400-53875400	Weak transcription	GM12878-XiMat	blood
18	chr3:53864800-53874400	Strong transcription	Fetal Intestine Small	intestine
19	chr3:53865600-53879800	Weak transcription	Aorta	Aorta
20	chr3:53867400-53875000	Genic enhancers	HepG2	liver
21	chr3:53867400-53876200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:53867600-53875200	Weak transcription	Stomach Mucosa	stomach
23	chr3:53867600-53875400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr3:53867600-53876400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr3:53867600-53876400	Weak transcription	Brain Substantia Nigra	brain
26	chr3:53867800-53875600	Weak transcription	Brain Anterior Caudate	brain
27	chr3:53869400-53876800	Weak transcription	Right Ventricle	heart
28	chr3:53869600-53879600	Weak transcription	Right Atrium	heart
29	chr3:53870200-53878600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr3:53870800-53875200	Weak transcription	Lung	lung
31	chr3:53870800-53875200	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr3:53870800-53879600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:53871600-53874400	Strong transcription	Liver	Liver
34	chr3:53871800-53876800	Weak transcription	HMEC	breast
35	chr3:53872800-53876200	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr3:53872800-53876400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr3:53872800-53877400	Weak transcription	Small Intestine	intestine
38	chr3:53873000-53874400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr3:53873200-53874400	Weak transcription	Fetal Stomach	stomach
40	chr3:53873200-53874800	Weak transcription	Fetal Intestine Large	intestine
41	chr3:53873200-53875400	Weak transcription	Brain Hippocampus Middle	brain
42	chr3:53873400-53875200	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr3:53873400-53876400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr3:53873600-53875200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr3:53873600-53875200	Weak transcription	Gastric	stomach
46	chr3:53873600-53875200	Weak transcription	Pancreas	Pancrea
47	chr3:53873600-53875600	Weak transcription	Brain Angular Gyrus	brain
48	chr3:53873800-53875200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:53873800-53876400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:53874000-53875400	Weak transcription	Duodenum Mucosa	Duodenum

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